BASys

BASys annotates bacterial chromosomal and plasmid DNA sequences to produce comprehensive gene and protein annotations for functional, structural, and metabolic analysis.

Key Features:

• Extensive Annotation: BASys employs over 30 distinct programs to generate approximately 60 annotation subfields per gene, including gene/protein names, Gene Ontology (GO) functions, Clusters of Orthologous Groups (COG) functions, predicted paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, predicted secondary and tertiary structures, biochemical reactions, and metabolic pathways.
• Input Types: Accepts raw DNA sequence data and optional gene-identification information for chromosomal and plasmid DNA.
• Comparative Annotation Quality: Produces annotations comparable to or exceeding the detail found in standard SwissProt entries.
• Processing Time: Generates comprehensive annotations in approximately 24 hours for an average bacterial genome (~5 Mb).

Scientific Applications:

• Functional annotation: Provides detailed functional assignments and annotations for newly sequenced bacterial genomes.
• Comparative genomics: Identifies orthologous and paralogous genes across species to support comparative genomics analyses.
• Structural biology: Supports protein structural investigations via predicted secondary and tertiary structures and subcellular localization.
• Metabolic pathway analysis: Identifies enzymes and biochemical reactions to map metabolic pathways.

Methodology:

BASys integrates multiple computational tools and databases, leveraging sequence alignment, homology modeling, and functional prediction algorithms.